Oxford Centre for
Computational Neuroscience
Professor Edmund T Rolls
https://www.oxcns.org
Automated Anatomical Labelling Atlas 3, AAL3v1
AAL3 User Guide
The automated anatomical parcellation AAL3 of the spatially normalized
single-subject high- resolution T1 volume provided by the Montreal Neurological
Institute (MNI). This includes the original parcellation provided in AAL (Tzourio-Mazoyer
et al., 2002), the new parcellation of the orbitofrontal
cortex provided in AAL2 (Rolls, Joliot, and Tzourio-Mazoyer (2015)) , but also new areas, as described in this
User Guide and by Rolls, Huang, Lin, Feng and Joliot
(2020).
Download
AAL3, released on the 27 August 2019: with an
update, named AAL3v1, in June 2020 involving small changes of the thalamic
parcellation in line with the update of Freesurfer 7.
SPM12 version of AAL3 software: AAL3v1_for_SPM12.zip
AAL3 is also available together
with AAL and AAL2 at http://www.gin.cnrs.fr/en/tools/aal/
User guide
Following a first
version AAL of the automated anatomical labeling atlas (Tzourio-Mazoyer et al
2002), a second version (AAL2) (Rolls, Joliot, and Tzourio-Mazoyer, 2015) was
developed that provided an alternative parcellation of the orbitofrontal cortex
following the description provided by Chiavaras, Petrides, and colleagues. We
now provide a third version, AAL3, which adds a number of brain areas not
previously defined, but of interest in many neuroimaging investigations. The
new areas in the third version are subdivision of the anterior cingulate cortex
into subgenual, pregenual and supracallosal parts; division of the thalamus
into its nuclei; the nucleus accumbens, substantia nigra, ventral tegmental
area, red nucleus, locus coeruleus, and raphe nuclei. The new atlas is
available as a toolbox for SPM, and can be used with MRIcron.
As in the previous
release of AAL, AAL3 is provided with isotropic voxel size 2x2x2 mm. In
addition, AAL3_1mm is also provided with a 1x1x1 mm voxel sampling size. Note
that only the AAL3 added regions benefit from this finer spatial definition.
## Please note that the original numbers in AAL2 for the anterior cingulate
cortex (35, 36) and thalamus (81, 82) are left empty in AAL3, as those voxels were substituted by the new
subdivisions (Thalamic nuclei: 121-151; ACC: 151-156). Thus, the total number
of parcellations in AAL3 is 166, with maximum label number 170. This ensures
that most of the numbers used in AAL2 remain the same in AAL3, while AAL3
mainly adds new areas starting at number 121.
## Please also note that caution is advised in the use of some of the
smaller regions defined in the AAL3, for reasons set out by Rolls, Huang, Lin,
Feng, and Joliot (2020). Further, if AAL3 was resampled to for example 3x3x3 mm, some of the smaller areas might no
longer be defined.
Content of the archive
1)
All the files with the “.m” extension are part of the code AAL3.m
2)
The nifti/gz files AAL3v1.nii / ROI_MNI_V7.nii / AAL3v1.nii.gz have the
same volume data, but the headers and compressions are different to accommodate
the needs of different types of software, which are AAL3 / spm (Results-Atlas)/ MRIcron respectively.
3)
The same applies to the 3 files: AAL3v1_1mm.nii / ROI_MNI_V7_1mm.nii /
AAL3v1_1mm.nii.gz
|
Atlas |
Filename |
description |
|
2x2x2 mm3 |
ROI_MNI_V7.nii |
Required for AAL3.m |
|
|
ROI_MNI_V7_vol.mat |
Required for AAL3.m |
|
|
ROI_MNI_V7_List.mat |
Required for AAL3.m |
|
|
ROI_MNI_V7_Border.mat |
Required for AAL3.m |
|
|
ROI_MNI_V7_vol.txt |
ROI description (text format) |
|
|
ROI_MNI_V7.xml |
ROI name (xml format) |
|
|
AAL3v1.nii.gz |
Required for mricron |
|
|
AAL3v1.nii.txt |
Required for mricron |
|
|
AAL3v1.nii |
Required for spm (Results-Atlas) |
|
|
AAL3v1.xml |
Required for spm (Results-Atlas) |
|
|
|
|
|
1x1x1 mm3 |
ROI_MNI_V7_1mm.nii |
Required for AAL3.m |
|
|
ROI_MNI_V7_1mm_vol.mat |
Required for AAL3.m |
|
|
ROI_MNI_V7_1mm_List.mat |
Required for AAL3.m |
|
|
ROI_MNI_V7_1mm_Border.mat |
Required for AAL3.m |
|
|
ROI_MNI_V7_1mm_vol.txt |
ROI description (text format) |
|
|
ROI_MNI_V7_1mm.xml |
ROI name (xml format) |
|
|
AAL3v1_1mm.nii.gz |
Required for mricron |
|
|
AAL3v1_1mm.nii.txt |
Required for mricron |
|
|
AAL3v1_1mm.nii |
Required for spm (Results-Atlas) |
|
|
AAL3v1_1mm.xml |
Required for spm (Results-Atlas) |
How to install the software on a unix system
1)
Copy the archive to the chosen location (e.g.
/usr/local/soft/spm12/toolbox) after removing the old AAL3 directory
unix> cp AAL3v1_for_SPM12.zip /usr/local/soft/spm12/toolbox
unix> cd /usr/local/soft/spm12/toolbox
2)
Gunzip and untar the archive will create an AAL3 directory
unix> unzip AAL3v1_for_SPM12.zip
3) Add this directory to your Matlab path and copy the 4 files in your SPM12/atlas
directory:
unix> mkdir /usr/local/soft/spm12/atlas
unix> cp /usr/local/soft/spm12/toolbox/AAL3/AAL3v1.nii
/usr/local/soft/spm12/atlas
unix> cp /usr/local/soft/spm12/toolbox/AAL3/AAL3v1.xml
/usr/local/soft/spm12/atlas
unix> cp /usr/local/soft/spm12/toolbox/AAL3/AAL3v1_1mm.nii
/usr/local/soft/spm12/atlas
unix> cp /usr/local/soft/spm12/toolbox/AAL3/AAL3v1_1mm.xml
/usr/local/soft/spm12/atlas
4) To install AAL3 for mricron software:
unix> cp /usr/local/soft/spm12/toolbox/AAL3/AAL3 v1.nii.gz /usr/local/soft/mricron/templates
unix> cp /usr/local/soft/spm12/toolbox/AAL3/AAL3 v1.nii.txt
/usr/local/soft/mricron/templates
unix> cp /usr/local/soft/spm12/toolbox/AAL3/AAL3v1_1mm.nii.gz
/usr/local/soft/mricron/templates
unix> cp /usr/local/soft/spm12/toolbox/AAL3/AAL3v1_1mm.nii.txt
/usr/local/soft/mricron/templates
(In Windows, copy the 4 files AAL3v1.nii.gz, AAL3v1.nii.txt and AAL3v1_1mm.nii.gz
and AAL3v1_1mm.nii.txt into mricron/templates.)
How to install the software on a Mac or Windows
system
The AAL3v1_for_SPM12.zip file is compatible with both Mac and Windows
systems. The installation is depending of your local installation of SPM and
Mricron software.
How to use the software
Both AAL3 (see 1)
or spm (see 2) can be used
Launch Matlab unix> matlab
1) Using
AAL3
1.1) how to launch
AAL3
- First option: launch AAL3 from SPM12:
Launch spm from the command window
>> spm fmri
In the SPM12 Menu window: “Results”
Select the desired contrast, mask, probability and extent threshold
In the SPM12 Menu window: “toolbox / AAL3”
- Second option: Launch AAL from the Matlab command window:
>> AAL3
Select the desired contrast, mask, probability and extent
threshold like in the regular spm Results.
1.2) Choose a labeling procedure. The 3 choices are
explained and documented in the paper (Tzourio-Mazoyer et al., 2002): Local
maxima labeling, Extended local maxima labeling and Cluster labeling.
For "Extended local maxima labeling" input the local maxima radius of
the sphere in millimeters (default 10 mm).
1.3) Select the
anatomical parcellation database
In /usr/local/soft/spm12/toolbox/AAL3
The file: ROI_MNI_V7.nii (2mm voxel edge, same file than AAL3v1)
or
The file: ROI_MNI_V7_1mm.nii (1mm voxel edge, same file than AAL3v1_1mm)
1.4) Then you get
the label on the coordinates in the Graphic window.
2) Using spm Atlas labelling function : “ spm (Results-Atlas)”
2.1) Launch spm from the command window
>> spm fmri
2.2) Select the desired contrast, mask, probability and
extent threshold in the regular “Results”. In the SPM12 Results window: Atlas /
Label using / AAL3v1
(You may in the SPM Graphics window need to right click
on the sections, and select Display > Labels > AAL3v1).
2.3) Then you get the label with a right click
on the coordinates in the Graphic window.
Original references
Automated Anatomical Labeling of Activations in
SPM Using a Macroscopic Anatomical Parcellation of the MNI MRI Single-Subject
Brain. N. Tzourio-Mazoyer, B. Landeau, D. Papathanassiou, F. Crivello, O.
Étard, N. Delcroix, B. Mazoyer, and M. Joliot. NeuroImage 2002. 15: 273-289. http://dx.doi.org/10.1006/nimg.2001.0978
Implementation of a new parcellation of the
orbitofrontal cortex in the automated anatomical labeling atlas. Rolls ET, Joliot M &
Tzourio-Mazoyer N (2015) NeuroImage 122: 1-5. http://dx.doi.org/10.1016/j.neuroimage.2015.07.075
References
Rolls, E.T., Huang, C.C., Lin, C.-P., Feng, J., Joliot, M., 2020. Automated anatomical labelling atlas 3,
Neuroimage 206:116189. https://doi.org/10.1016/j.neuroimage.2019.116189